Researchers have recovered variola virus DNA from two naturally mummified Indigenous individuals in northern Chile, providing the first solid genetic proof that European colonizers introduced smallpox to the Americas. The findings, published in Science, match historical accounts of catastrophic population decline while revealing unexpected evolutionary shifts in the pathogen.
For centuries, the narrative of how smallpox devastated the Americas relied almost entirely on a paper trail of colonial writings, administrative records, and missionary reports. While those documents left little doubt that the disease wiped out millions of Indigenous people who lacked immune protection, actual molecular proof remained missing. That changed when a team of researchers examining archaeological remains in northern Chile recovered smallpox viral DNA.
The discovery emerged unexpectedly from bone samples previously collected at Camarones 9, an archaeological site in northern Chile. Investigators were initially looking to understand human population history when they uncovered traces of a smallpox variant. The viral genomes were pulled from the leg bone fragments of an adult woman and an adult man estimated to have died between 1492 and 1631 CE.
Uncovering the CAM9 Strain and Its European Roots
The genetic material recovered from the two mummies proved to be almost identical, indicating that both individuals contracted the infection during the same outbreak or from the same circulating strain. Because the virus lineage was entirely unknown in the region’s historical timeline, researchers designated the new strain CAM9.
By comparing the CAM9 genomes against both ancient and modern variola virus sequences, scientists fitted the strain neatly between medieval European variants and later forms of the disease. This molecular positioning demonstrates that the smallpox variants infecting populations in the Americas evolved first from Europe, offering concrete scientific confirmation of an event long accepted through historical extrapolation.
“Nobody would ever question that smallpox came to this hemisphere from colonization, but this proves it.”
Patricia Foster, biologist at Indiana University, via AP News
Working with ancient viral genomes presents formidable hurdles. Biological anthropologist Constanza de la Fuente Castro of the University of Chile noted that investigators faced severe degradation issues due to low DNA concentration and centuries of accumulated chemical damage.
“We are working with DNA that is in low concentration and has accumulated damage over time. This is affecting our ability to recover it, but it is also challenging to analyze.”
Constanza de la Fuente Castro, biological anthropologist at the University of Chile, via ScienceAlert
Tracking Viral Evolution Across Centuries of Colonization
Beyond confirming the historical vector of the disease, the CAM9 genomes provide a rare snapshot into how pathogens adapt when encountering immunologically naive populations. Genomicist Shigeki Nakagome of Trinity College Dublin pointed out that the viral lineage serves as a snapshot of the viral evolution, helping researchers understand which genetic modifications occurred before the pathogen reached the Americas during early colonial times versus those that developed later.
The analysis revealed a surprising phase in the pathogen’s lifecycle. After initial contact, the mutation rate of the smallpox virus slowed dramatically for approximately two centuries.
Broader Scientific Implications and Regional Preservation
The implications of recovering ancient viral DNA extend beyond historical validation. Studying how variola virus shed unnecessary genes as it specialized for human hosts provides valuable comparative data for related modern pathogens, such as the virus that causes mpox.
The discovery also underscores the human toll documented by the physical remains of the two individuals, who were between 18 and 35 years old when the disease likely claimed their lives. De la Fuente Castro emphasized that the catastrophe is literally written into biological evidence preserved across generations.
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